Multivar_Mine Report
INDIVIDUAL SOURCE ANALYSIS (mfa)
GI_Functions (pca)
Dimensionality reduction
This section encompasses a general overview of the dimensionality reduction analysis applied.
Inertia plot: % of total variance by PC
Graphical representation of Principal Components (PCs). Line represents accumulated explained variance. Only significant PCs will be considered in the following plots.
Sample coordinates
This plot represents the coordinates of the samples on the two first Principal Components (Dim1 and Dim2) along with percentage of explained variance.
Categorical variables
This section explore the relationship between supplementary categorical variables (-S option), samples and PCs.
Any supplementary qualitative variable was included on this analysis. Any supplementary quantitative variable was included on this analysis.TOP active quantitative variables
This table summarizes the top 10 active quantitative variables associated with PCs.HCPC
This section explore the groups of samples based on Hierarchical Clustering on Principal Components (HCPC) and the relationship of the clusters with supplementary variables. For the HCPC only the 18 first relevant PCs where used.Hierarchical clustering of individuals18 significant PCs
This plot represent the dendrogram of HCPC of the individuals. The groups of individuals have different colors and the inertia plot is showed at the top right.
HCPC coordinates
This plot represent the coordinates of the samples in the two main Principal Components. The percentage of summarized variance is showed between brackets. The samples are colored by their HCPC cluster.
Relationship between HCPC clusters and supplementary qualitative variables
Fisher's exact test is computed between clusters and experimental treats. Fisher's exact test P values and FDR are showed.None of the clusters was significanstly associated with any experimental group
Whole_Genome_Functions (pca)
Dimensionality reduction
This section encompasses a general overview of the dimensionality reduction analysis applied.
Inertia plot: % of total variance by PC
Graphical representation of Principal Components (PCs). Line represents accumulated explained variance. Only significant PCs will be considered in the following plots.
Sample coordinates
This plot represents the coordinates of the samples on the two first Principal Components (Dim1 and Dim2) along with percentage of explained variance.
Categorical variables
This section explore the relationship between supplementary categorical variables (-S option), samples and PCs.
Any supplementary qualitative variable was included on this analysis. Any supplementary quantitative variable was included on this analysis.TOP active quantitative variables
This table summarizes the top 10 active quantitative variables associated with PCs.HCPC
This section explore the groups of samples based on Hierarchical Clustering on Principal Components (HCPC) and the relationship of the clusters with supplementary variables. For the HCPC only the 6 first relevant PCs where used.Hierarchical clustering of individuals6 significant PCs
This plot represent the dendrogram of HCPC of the individuals. The groups of individuals have different colors and the inertia plot is showed at the top right.
HCPC coordinates
This plot represent the coordinates of the samples in the two main Principal Components. The percentage of summarized variance is showed between brackets. The samples are colored by their HCPC cluster.
Relationship between HCPC clusters and supplementary qualitative variables
Fisher's exact test is computed between clusters and experimental treats. Fisher's exact test P values and FDR are showed.None of the clusters was significanstly associated with any experimental group
Relative_Mobilome_Number (pca)
Dimensionality reduction
This section encompasses a general overview of the dimensionality reduction analysis applied.
Inertia plot: % of total variance by PC
Graphical representation of Principal Components (PCs). Line represents accumulated explained variance. Only significant PCs will be considered in the following plots.
Sample coordinates
This plot represents the coordinates of the samples on the two first Principal Components (Dim1 and Dim2) along with percentage of explained variance.
Categorical variables
This section explore the relationship between supplementary categorical variables (-S option), samples and PCs.
Any supplementary qualitative variable was included on this analysis. Any supplementary quantitative variable was included on this analysis.TOP active quantitative variables
This table summarizes the top 10 active quantitative variables associated with PCs.HCPC
This section explore the groups of samples based on Hierarchical Clustering on Principal Components (HCPC) and the relationship of the clusters with supplementary variables. For the HCPC only the 2 first relevant PCs where used.Hierarchical clustering of individuals2 significant PCs
This plot represent the dendrogram of HCPC of the individuals. The groups of individuals have different colors and the inertia plot is showed at the top right.
HCPC coordinates
This plot represent the coordinates of the samples in the two main Principal Components. The percentage of summarized variance is showed between brackets. The samples are colored by their HCPC cluster.
Relationship between HCPC clusters and supplementary qualitative variables
Fisher's exact test is computed between clusters and experimental treats. Fisher's exact test P values and FDR are showed.None of the clusters was significanstly associated with any experimental group
INTEGRATIVE ANALYSIS
MFA analysis
Dimensionality reduction
This section encompasses a general overview of the dimensionality reduction analysis applied.
Inertia plot: % of total variance by PC
Graphical representation of Principal Components (PCs). Line represents accumulated explained variance. Only significant PCs will be considered in the following plots.
Individual PCs contribution
This plot represents the Pearson's correlation between the PCs from the individual dimensionality reduction analysis of the variable groups and the two main integrated PCs (Dim1 and Dim2). The color represent the different variable groups and the variance summarized by the integrated PC is showed between brackets.
Representation of the sample coordinates on the two first integrated PCs
This plot represents the coordinates of the samples on the two first integrated PCs (Dim1 and Dim2) as a black dot. The colored dots represent the coordinates of the samples for each active group of variables and the colored lines represent its distance from the integrated coordinates. The variance summarized by the two first integrated PCs is showed betwwen brackets.
Categorical variables
This section explore the relationship between supplementary categorical variables (-S option), samples and PCs.
Any supplementary qualitative variable was included on this analysis.Coordinates of categories
This plot represent the coordinates of the samples and supplementary categories on the two first Principal Components (Dim1 and Dim2). The samples are represented in blue and the categories of each supplementary group have the same color. The percentage of explained variance is given between brackets.
TOP active qualitative variables
This table summarizes the top 10 active qualitative variables associated with PCs.None of the categories was significantly associated with any PC Any supplementary quantitative variable was included on this analysis.
TOP active quantitative variables
This table summarizes the top 10 active quantitative variables associated with PCs.HCPC
This section explore the groups of samples based on Hierarchical Clustering on Principal Components (HCPC) and the relationship of the clusters with supplementary variables. For the HCPC only the 22 first relevant PCs where used.Hierarchical clustering of individuals22 significant PCs
This plot represent the dendrogram of HCPC of the individuals. The groups of individuals have different colors and the inertia plot is showed at the top right.
HCPC coordinates
This plot represent the coordinates of the samples in the two main Principal Components. The percentage of summarized variance is showed between brackets. The samples are colored by their HCPC cluster.
Relationship between HCPC clusters and supplementary qualitative variables
Fisher's exact test is computed between clusters and experimental treats. Fisher's exact test P values and FDR are showed.None of the clusters was significanstly associated with any experimental group